Sharp Increase of Problematic Mitogenomes of Birds: Causes, Consequences, and Remedies

Authentic DNA sequences are crucial for reliable evolutionary inference. Concerns about the identification of DNA sequences have been voiced several times in the past but few quantitative studies exist. Mitogenomes play important roles in phylogenetics, phylogeography, population genetics, and DNA identification. However, the large number of mitogenomes being published routinely, often in brief data papers, has raised questions about their authenticity. In this study, we quantify problematic mitogenomes of birds and their reusage in other papers. Of 1,876 complete or partial mitogenomes of birds published until January 1, 2020, the authenticity of 1,559 could be assessed with sequences of conspecifics. Of these, 78 (5.0%) were found to be problematic, including 45 curated reference sequences. Problems were due to misidentification (33), chimeras of two or three species (23), sequencing errors/numts (18), incorrect sequence assembly (1), mislabeling at GenBank but not in the final paper (2), or vice versa (1). The number of problematic mitogenomes has increased sharply since 2012. Worryingly, these problematic sequences have been reused 436 times in other papers, including 385 times in phylogenies. No less than 53% of all mitogenomic phylogenies/networks published until January 1, 2020 included at least one problematic mitogenome. Problematic mitogenomes have resulted in incorrect phylogenetic hypotheses and proposals for unwarranted taxonomic revision, and may have compromised comparative analyses and measurements of divergence times. Our results indicate that a major upgrade of quality control measures is warranted. We propose a comprehensive set of measures that may serve as a new standard for publishing mitogenome sequences.

Who owns your DNA?

With the recent news that George Church is selling his genome as a nonfungible token and more unresolved murder cases being solved through familial DNA identification, BioTechniques is asking: who owns your DNA?

Universal Set of Primers for DNA Identification of Alien Fish Species in Central Russia (Volga-Kama Region)

Reliable species identification is critical for detection and monitoring of biological invasions. In this study, we propose four sets of primers for efficient amplification of several loci, including the mitochondrial cytochrome oxidase-c (COI) subunit I gene which is a basis for DNA barcoding. This set of primers gives a shorter product which can be used in high-throughput sequencing systems for metabarcoding purposes. Another mitochondrial locus encoding the large ribosomal subunit (16S) may be useful to study the population structure and as an additional source of information in the metabarcoding of communities. We propose to use a set of primers for the nuclear locus of the small ribosomal subunit (18S) as a positive control and to verify the results of the barcoding. Our proposed sets of primers demonstrate a high amplification efficiency and a high specificity both for freshwater alien and indigenous fishes. The proposed research design makes it possible to carry out extremely cheap studies on the assessment of biological diversity using genetic analysis without expensive equipment, and with the technique for conducting laboratory work and processing of the results available to any researcher. The paper also presents original data on the genetic polymorphism of all mass alien fish species in the Volga-Kama region. High efficiency of DNA identification based on our primers is shown as compared to traditional monitoring of biological invasions.

Comparison of the Allelic Alterations between InDel and STR Markers in Tumoral Tissues Used for Forensic Purposes

Background and objectives: Over the last two decades, human DNA identification and kinship tests have been conducted mainly through the analysis of short tandem repeats (STRs). However, other types of markers, such as insertion/deletion polymorphisms (InDels), may be required when DNA is highly degraded. In forensic genetics, tumor samples may sometimes be used in some cases of human DNA identification and in paternity tests. Nevertheless, tumor genomic instability related to forensic DNA markers should be considered in forensic analyses since it can compromise genotype attribution. Therefore, it is useful to know what impact tumor transformation may have on the forensic interpretation of the results obtained from the analysis of these polymorphisms. Materials and Methods: The aim of this study was to investigate the genomic instability of InDels and STRs through the analysis of 55 markers in healthy tissue and tumor samples (hepatic, gastric, breast, and colorectal cancer) in 66 patients. The evaluation of genomic instability was performed comparing InDel and STR genotypes of tumor samples with those of their healthy counterparts. Results: With regard to STRs, colorectal cancer was found to be the tumor type affected by the highest number of mutations, whereas in the case of InDels the amount of genetic mutations turned out to be independent of the tumor type. However, the phenomena of genomic instability, such as loss of heterozygosity (LOH) and microsatellite instability (MSI), seem to affect InDels more than STRs hampering genotype attribution. Conclusion: We suggest that the use of STRs rather than InDels could be more suitable in forensic genotyping analyses given that InDels seem to be more affected than STRs by mutation events capable of compromising genotype attribution.

DNA polymorphism of dogs (Canis familiaris L.). III. VNTR- and STR-loci. Their use in dog breeding and in criminalistics.

The application of mini- and microsatellite polymorphisms of dog DNA, also referred to as VNTR- and STR-loci, respectively, in dog breeding and criminalistics is considered. Their use in dog breeding is shown to clarify pedigrees, establish paternity and purebred, as well as to differentiate breeds mainly in the form of microsatellite DNA polymorphism. In criminalistics, dogs can be both participants in crime scenes in the form of attacks on humans or pets, and some witnesses through whose DNA extracted from their fur or feces, by DNA identification of a particular dog, it may be help to get out to the perpetrator or at least to the crime scene, which is also a good help in its disclosure. At the same time, population studies of dogs, during which the prevalence of certain alleles of marker traits in the form of STR loci in different territories is established, contribute to making the right decisions. The databases on STR-polymorphism of dog DNA or their prototypes are briefly described. Attention is paid to the sources of forensic canine DNA, as well as methods of its extraction and preliminary evaluation of isolated preparations. The use of VNTR polymorphism was rather short-lived, and was quickly replaced by STR polymorphism. There are some trends in the introduction of new polymorphic traits in this area in the form of single-nucleotide polymorphism or SNPs, potentially providing more accurate information, including for DNA identification of individuals. The issues of universal DNA certification of dogs are discussed, which can contribute to improving the culture of keeping dogs and will allow the elimination of stray dogs in the future, which will be humanistic character and potentially reduce the number of aggressor dogs.

DNA Identification, Joint Rights and Collective Responsibility

DNA identification developed late in the twentieth century and has surpassed fingerprinting as the leading technique for forensic human identification. It differs from the other biometrics discussed in that it is based on principles of biological, rather than physical sciences. Another difference is the time taken to convert a biological sample into a DNA profile; however, this is becoming less significant as technology progresses. DNA is also more accurate and revealing in comparison with other biometrics because it can provide information about a person’s physical appearance and health status, as well as link an individual to, and in association with further investigations, identify, their biological relatives. This chapter examines DNA identification in law enforcement, related developments associated with commercial genomic health and ancestry databases, and the potential impact of population wide DNA collection. The ethical analysis considers privacy and autonomy, self-incrimination, joint rights and collective responsibility.